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If you try the same delete using Windows Explorer, do you see additional error messages or warning prompts?

BC3 should be able to delete a System folder or file, but will present a dialog prompt warning you it is a System file/folder by default. You can verify this by creating a test folder and file on your Desktop, then using BC3 or Explorer to assign the System attribute to them.
However, these System folders you are attempting to delete must have been marked by the system, and may be protected by the Operating System in other ways.